Contacts of the helix formed by residues 299 - 310 (chain C) in PDB entry 5G04
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 299 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267C SER* 2.9 29.0 + - - +
271C VAL* 3.7 16.9 - - + +
286C PHE* 4.1 8.8 - - + -
289C LEU* 5.3 0.7 - - + -
296C ARG* 2.7 24.3 + - - +
298C GLU* 1.3 86.8 + - - +
300C MET* 1.3 63.7 + - - +
301C ASP 3.2 3.4 - - - +
302C THR* 3.0 40.4 + - + +
303C PHE* 3.4 6.2 + - - +
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Residues in contact with MET 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C PHE* 4.9 2.7 - - - -
289C LEU* 4.9 11.0 - - + -
290C ARG* 3.4 39.5 - - + +
293C ASP 5.0 0.4 - - - +
296C ARG* 4.0 37.7 - - + +
297C ILE* 3.3 12.9 + - - +
299C ASN* 1.3 80.5 - - - +
301C ASP* 1.4 66.5 + - - +
303C PHE* 3.4 21.6 - - + +
304C SER* 2.9 25.6 + - - -
319C LEU* 3.7 18.9 - - + +
323C LEU* 3.8 23.8 - - + -
332C GLU* 5.2 0.4 - - + -
336C VAL* 3.4 4.0 - - + +
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Residues in contact with ASP 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298C GLU 5.7 0.2 - - - +
299C ASN* 3.2 2.2 - - - +
300C MET* 1.4 79.7 - - - +
302C THR* 1.3 62.5 - - - +
304C SER* 3.4 1.6 - - - -
305C ASN* 3.2 26.1 + - - +
332C GLU* 4.1 26.4 - - + +
335C CYS* 3.0 42.9 - - - +
336C VAL* 3.6 5.3 + - - +
339C ASN* 3.9 6.1 + - - -
364C TYR* 2.5 40.8 + - + +
79R TYR* 5.1 1.0 + - - -
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Residues in contact with THR 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C VAL* 4.0 19.4 - - + -
274C HIS* 3.6 31.1 + - - +
286C PHE* 3.8 11.1 - - + -
299C ASN* 3.0 39.5 - - + +
301C ASP* 1.3 71.7 - - - +
303C PHE* 1.3 63.9 - - - +
305C ASN* 3.2 20.1 + - - +
306C LEU* 3.3 13.5 + - - +
364C TYR* 5.2 1.2 + - - -
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Residues in contact with PHE 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C LEU* 4.3 9.9 - - + -
286C PHE* 3.4 65.8 - + + -
287C ASN* 3.7 24.0 - - - -
290C ARG* 3.8 22.7 - - + -
299C ASN 3.4 5.1 + - - -
300C MET* 3.2 35.4 + - + +
302C THR* 1.3 75.2 - - - +
304C SER* 1.3 63.7 + - - +
306C LEU* 3.3 3.8 + - - +
307C LEU* 3.0 45.8 + - + -
319C LEU* 4.3 8.1 - - + -
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Residues in contact with SER 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C MET 2.9 16.5 + - - -
301C ASP 3.4 2.9 - - - -
303C PHE* 1.3 74.4 - - - +
305C ASN* 1.3 61.6 + - - +
307C LEU* 3.5 1.9 - - - +
308C TYR* 2.8 30.8 + - - +
316C LEU* 3.3 21.2 - - - +
319C LEU* 4.0 5.6 - - - +
336C VAL* 3.6 20.5 - - - -
339C ASN* 2.7 37.8 + - - +
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Residues in contact with ASN 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C HIS* 4.5 15.1 + - + -
301C ASP* 3.2 19.1 + - - +
302C THR* 3.2 16.9 + - - +
304C SER* 1.3 79.6 - - - +
306C LEU* 1.3 60.7 + - - +
308C TYR* 3.3 4.0 + - - +
309C VAL* 3.2 17.5 + - - +
339C ASN* 3.7 16.5 + - - +
364C TYR* 5.4 0.8 + - - -
370C LEU* 4.4 5.3 - - - +
78R ARG* 3.2 39.3 + - + +
79R TYR* 3.0 38.4 + - - -
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Residues in contact with LEU 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274C HIS* 4.1 26.2 - - + +
279C ILE* 4.0 28.0 - - + +
282C ALA* 3.9 24.5 - - + -
283C LEU* 2.8 40.3 - - + +
286C PHE* 3.7 30.5 - - + -
302C THR 3.3 1.9 + - - +
303C PHE 3.3 11.8 + - - +
305C ASN* 1.3 75.8 - - - +
307C LEU* 1.3 69.5 + - - +
309C VAL* 3.4 14.6 + - - +
310C ARG* 3.4 10.4 + - - +
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Residues in contact with LEU 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C LEU* 4.8 5.6 - - + -
303C PHE* 3.0 44.1 + - + +
304C SER 3.5 4.5 - - - +
306C LEU* 1.3 84.1 - - - +
308C TYR* 1.3 61.5 + - - +
310C ARG* 3.4 3.0 + - - -
311C SER 3.2 14.9 + - - -
312C MET* 3.0 51.6 + - + +
315C GLU* 3.9 11.4 - - + +
316C LEU* 3.4 39.9 - - + +
319C LEU* 3.9 8.7 - - + -
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Residues in contact with TYR 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304C SER 2.8 17.3 + - - +
305C ASN* 3.4 4.5 - - - +
306C LEU 3.2 0.2 - - - -
307C LEU* 1.3 77.4 - - - +
309C VAL* 1.3 57.6 + - - +
311C SER* 3.1 17.7 + - - +
316C LEU* 4.0 11.6 - - + +
339C ASN* 3.5 15.9 - - + -
342C SER* 2.9 30.2 + - - -
343C LEU* 3.3 39.3 - - + -
347C HIS* 4.7 4.7 + - - -
374C GLU* 5.3 1.0 + - - -
377C GLU* 5.3 4.7 + - - -
78R ARG* 2.9 49.8 + - + +
129R LYS* 6.1 0.5 - - - +
133R LEU* 3.6 35.8 + - + +
134R SER* 4.0 7.1 + - - -
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Residues in contact with VAL 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C ILE* 4.7 12.3 - - + -
305C ASN 3.2 8.3 + - - +
306C LEU* 3.8 11.4 - - - +
307C LEU 3.3 0.4 - - - -
308C TYR* 1.3 73.1 - - - +
310C ARG* 1.3 69.6 + - + +
311C SER* 3.1 6.7 + - - -
75R GLY 4.8 1.6 - - - +
76R GLY* 3.0 29.9 - - - +
77R ASP* 3.5 4.5 - - - -
78R ARG* 3.2 50.3 - - + +
133R LEU* 3.9 19.6 - - + +
134R SER* 4.3 11.4 - - - +
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Residues in contact with ARG 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C ILE* 3.4 34.9 - - + +
280C ASP* 2.9 43.7 + - - +
283C LEU* 3.6 24.8 - - + +
306C LEU 3.4 7.4 + - - +
307C LEU* 3.4 4.7 + - - +
308C TYR 3.4 0.2 - - - -
309C VAL* 1.3 81.6 - - + +
311C SER* 1.3 67.0 + - - +
312C MET* 3.2 24.1 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il